From d144517e56acb7d36c08038c0363dca9222c10a6 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Tue, 4 Feb 2025 15:26:31 +0100
Subject: [PATCH 1/2] ref_period and NA bug

---
 R/PeriodStandardization.R | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index b71270f..d9cedb2 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -87,7 +87,7 @@
 #'class(data) <- 's2dv_cube'
 #'SPEI <- CST_PeriodStandardization(data = data)
 #'@export
-CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', 
+CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', dates = NULL, 
                                       leadtime_dim = 'time', memb_dim = 'ensemble',
                                       ref_period = NULL,
                                       handle_infinity = FALSE, 
@@ -125,7 +125,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
 
   if (is.null(data_cor)) {
     data$data <- std
-    data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, ' standardized')
+    data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname
+    if (!is.null(data_longname)) {
+      data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized')
+    }
     if (return_params) {
       return(list(spei = data, params = params))
     } else {
@@ -133,7 +136,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
     }
   } else {
     data_cor$data <- std
-    data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, ' standardized')
+    data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname
+    if (!is.null(data_cor_longname)) {
+      data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized')
+    }
     data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets)
     data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files)
     return(data_cor)
@@ -611,8 +617,8 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   }
   if (handle_infinity) { 
     # could also use "param_error" ?; we are giving it the min/max value of the grid point
-    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)])
-    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)]) 
+    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = T)
+    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = T) 
   }
   if (return_params) {
     return(list(spei = spei_mod, params = params_result))
@@ -644,4 +650,4 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   } else {
     return(NA)
   }
-}
\ No newline at end of file
+}
-- 
GitLab


From f4897b6b55571d197b2ceb32db5fdf95f63997d3 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Fri, 7 Feb 2025 12:29:27 +0100
Subject: [PATCH 2/2] na.rm in max/min()

---
 .Rbuildignore             | 2 ++
 .gitignore                | 1 +
 R/PeriodStandardization.R | 6 +++---
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 2a2a753..da90668 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,3 +12,5 @@
 ^cran-comments\.md$
 ./vignettes/*.md
 ^inst/doc/paper-figure-PlotForecastPDF\.R$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index 23a5603..022a306 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,3 +18,4 @@ Rplots.pdf
 *.RData
 !data/*.RData
 .\.nfs*
+.Rproj.user
diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index d9cedb2..dcef847 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -87,7 +87,7 @@
 #'class(data) <- 's2dv_cube'
 #'SPEI <- CST_PeriodStandardization(data = data)
 #'@export
-CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', dates = NULL, 
+CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', 
                                       leadtime_dim = 'time', memb_dim = 'ensemble',
                                       ref_period = NULL,
                                       handle_infinity = FALSE, 
@@ -617,8 +617,8 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   }
   if (handle_infinity) { 
     # could also use "param_error" ?; we are giving it the min/max value of the grid point
-    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = T)
-    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = T) 
+    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = TRUE)
+    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = TRUE) 
   }
   if (return_params) {
     return(list(spei = spei_mod, params = params_result))
-- 
GitLab